It should. Can you send me the pdb file, and I'll try and figure out what's
wrong?
On 2 February 2011 10:13, Noel O'Boyle <baoille...@gmail.com> wrote:
> No dice. I killed "obabel 2GDZ.pdb -O 2GDZ.pdbqt -xr" after 4.5 mins.
> Presumably it should only take a few seconds max?
>
> - Noel
>
> On 1 February 2011 14:49, Stuart Armstrong <stuart.armstr...@inhibox.com>
> wrote:
> > Dear Noel,
> > Have you tried running it with the -xr option? It sounds like it's trying
> to
> > construct the torsion tree, which would take a huge amount of time for a
> > protein. With 'r' it should output rigidly.
> > Let me know if this helps,
> > Stuart
> >
> > On 28 January 2011 14:42, Noel O'Boyle <baoille...@gmail.com> wrote:
> >>
> >> Hi all,
> >>
> >> I've just been trying to prepare a protein for setting up a docking
> >> with Autodock. Is this pdbqt format intended for this or is it just
> >> for the ligands? The description in the help message is somewhat
> >> minimal.
> >>
> >> In any case, I tried to do this conversion but after several minutes
> >> waiting I terminated it and filed a bug:
> >>
> >>
> https://sourceforge.net/tracker/?func=detail&aid=3167053&group_id=40728&atid=428740
> .
> >>
> >> Am I doing something wrong?
> >>
> >> - Noel
> >>
> >> On 1 September 2010 14:52, Stuart Armstrong
> >> <stuart.armstr...@inhibox.com> wrote:
> >> > Dear Open Babel,
> >> > Included here is the pdbqtformat.cpp file, which has read and write
> >> > capabilities. The help message (babel -Hpdbqt) gives the options and
> >> > reads:
> >> > pdbqt Autodock Protein Data Bank Q (Partial Charge) & Type
> >> > Read Options e.g. -ab, -abd
> >> > b Disable automatic bonding
> >> > d Input file is in dlg (docking log file) format.
> >> > Write options, e.g. -xr, -xp, -xrp
> >> > b Enables automatic bonding before writing to pdbqt format
> >> > r Outputs rigid molecule (no branches)
> >> > s Outputs as a flexible residue
> >> > p Preserves the atom indexes from the input file (default is to
> >> > renumber
> >> > sequentially).
> >> >
> >> > Specification at:
> >> >
> >> >
> http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file
> >> > ------------------------------
> >> >
> >> > The file makes use of atom and bond indexes, as its method involves
> >> > deleting
> >> > atoms and bonds one at a time and counting the remaining pieces; this
> is
> >> > done by copying the molecule and operating on the copy, with the
> indexes
> >> > used to identify the relevant components in the original molecule
> >> > object.
> >> > Tomorrow I should be able to send you a message confirming that you
> are
> >> > free
> >> > to distribute the file (let me know if you require anything more).
> >> > All the best,
> >> > Stuart
> >
> >
>
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